SYNOPSIS

DESCRIPTION

Object which presents a literature reference. This is considered to be a specialised form of database link. The additional methods provided are all set/get methods to store strings commonly associated with references, in particular title, location (ie, journal page) and authors line.

There is no attempt to do anything more than store these things as strings for processing elsewhere. This is mainly because parsing these things suck and generally are specific to the specific format one is using. To provide an easy route to go format --> object --> format without losing data, we keep them as strings. Feel free to post the list for a better solution, but in general this gets very messy very fast...

AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

AnnotationI implementing functions

as_text

Title : as_text
Usage :
Function:
Example :
Returns :
Args :

display_text

Title : display_text
Usage : my $str = $ann->display_text();
Function: returns a string. Unlike as_text(), this method returns a string
formatted as would be expected for te specific implementation.
One can pass a callback as an argument which allows custom text
generation; the callback is passed the current instance and any text
returned
Example :
Returns : a string
Args : [optional] callback

hash_tree

Title : hash_tree
Usage :
Function:
Example :
Returns :
Args :

tagname

Title : tagname
Usage : $obj->tagname($newval)
Function: Get/set the tagname for this annotation value.
Setting this is optional. If set, it obviates the need to provide
a tag to Bio::AnnotationCollectionI when adding this object. When
obtaining an AnnotationI object from the collection, the collection
will set the value to the tag under which it was stored unless the
object has a tag stored already.
Example :
Returns : value of tagname (a scalar)
Args : new value (a scalar, optional)

rp

rg

Title : rg
Usage : $obj->rg($newval)
Function: Gives the RG line. This is Swissprot/Uniprot specific, and
if set will usually be identical to the authors attribute,
but the swissprot manual does allow both RG and RA (author)
to be present for the same reference.
Example :
Returns : value of rg (a scalar)
Args : on set, new value (a scalar or undef, optional)

gb_reference

Title : gb_reference
Usage : $obj->gb_reference($newval)
Function: Gives the generic GenBank REFERENCE line. This is GenBank-specific.
If set, this includes everything on the reference line except
the REFERENCE tag and the reference count. This is mainly a
fallback for the few instances when REFERENCE lines have unusual
additional information such as split sequence locations, feature
references, etc. See Bug 2020 in Bugzilla for more information.
Example :
Returns : value of gb_reference (a scalar)
Args : on set, new value (a scalar or undef, optional)